Pemberton, J. M. | bioRxiv Science

bioRxiv2018

A genomic region containing REC8 and RNF212B is associated with individual recombination rate variation in a wild population of red deer (Cervus elaphus)

Recombination is a fundamental feature of sexual reproduction, ensuring proper disjunction, preventing mutation accumulation and generating new allelic combinations upon which selection can act. However it is also mutagenic, and breaks up favourable allelic combinations previously built up by selection. Identifying the genetic drivers of recombination rate variation is a key step in understanding the causes and consequences of this variation, how lociassociated with recombination are evolving and how they affect the potential of a population to respond to selection. However, to date, few studies have examined the genetic architecture of recombination rate variation in natural populations. Here, we use pedigree data from -2,600 individuals genotyped at -38,000 SNPs to investigate the genetic architecture of individual autosomal recombination rate in a wild population of red deer (Cervus elaphus). Female red deer exhibited a higher mean and phenotypic variance in autosomal crossover counts (ACC). Animal models fitting genomic relatedness matrices showed that ACC was heritable in females (h2 = 0.12) but not in males. A regional heritability mapping approach showed that almost all heritable variation in female ACC was explained by a genomic region on deer linkage group 12 containing the candidate loci REC8 and RNF212B, with an additional region on linkage group 32 containing TOP2B approaching genome-wide significance. The REC8/RNF212B region and its paralogue RNF212 have been associated with recombination in cattle, mice, humans and sheep. Our findings suggest that mammalian recombination rates have a relatively conserved genetic architecture in both domesticated and wild systems, and provide a foundation for understanding the association between recombination lociand individual fitness within this population.

genetics↗

bioRxiv2017

A high-density linkage map reveals sexually-dimorphic recombination landscapes in red deer (Cervus elaphus)

High density linkage maps are an important tool to gain insight into the genetic architecture of traits of evolutionary and economic interest, and provide a resource to characterise variation in recombination landscapes. Here, we used information from the cattle genome and the 50K Cervine Illumina BeadChip to inform and refine a high density linkage map in a wild population of red deer (Cervus elaphus). We constructed a predicted linkage map of 38,038 SNPs and a skeleton map of 10,835 SNPs across 34 linkage groups. We identified several chromosomal rearrangements in the deer lineage relative to sheep and cattle, including six chromosome fissions, one fusion and two large inversions. Otherwise, our findings showed strong concordance with map orders in the cattle genome. The sex-averaged linkage map length was 2739.7cM and the genome-wide autosomal recombination rate was 1.04cM per Mb. The female autosomal map length was 1.21 longer than that of males (2767.4cM vs 2280.8cM, respectively). Sex differences in map length were driven by high female recombination rates in peri-centromeric regions, a pattern that is unusual relative to other mammal species. This effect was more pronounced in fission chromosomes that would have had to produce new centromeres. We propose two hypotheses to explain this effect: (1) that this mechanism may have evolved to counteract centromeric drive associated with meiotic asymmetry in oocyte production; and/or (2) that sequence and structural characteristics suppressing recombination in close proximity to the centromere may not have yet evolved at neo-centromeres. Our study provides insight into how recombination landscapes vary and evolve in mammals, and will provide a valuable resource for studies of evolution, genetic improvement and population management in red deer and related species.\n\nArticle SummaryWe present a high density linkage map (>38,000 markers) in a wild population of Red deer (Cervus elaphus). Our investigation of the recombination landscape showed a marked difference in recombination rates between the sexes in proximity to the centromere, with females showing an unusually elevated rate relative to other mammal species. This effect is most pronounced in chromosomes that would have produced a new centromere in the deer lineage. We propose that the observed effects have evolved to counteract selfish genetic elements associated with asymmetrical female meiosis.

genomics↗